Nmr bucketing3 #243
Nmr bucketing3 #243
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… direct bucketing
… the "Input file" parameter
… of a tsv file possibility
Fix a syntax error
remove R deps bump version add log change
Update changelog
…graphical representation modification
…of input files (if zip = printing; else = no printing)
…omed" windows depending on exclusion borders
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ping @mtremblayfr |
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Thanks @lecorguille and @mtremblayfr.
I have added some comments inline. Greeting from the Australian Cofest!
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| <tool id="NmrBucketing" name="NMR_Bucketing" version="2.0.3"> | |||
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| <tool id="NmrBucketing" name="NMR_Bucketing" version="2.0.3"> | |
| <tool id="NmrBucketing" name="NMR_Bucketing" version="2.0.3" profile="21.05"> | |
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| <tool id="NmrBucketing" name="NMR_Bucketing" version="2.0.3"> | |||
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| <description> Bucketing and integration of NMR Bruker raw data</description> | |||
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| <description> Bucketing and integration of NMR Bruker raw data</description> | |
| <description>Bucketing and integration of NMR Bruker raw data</description> | |
| <stdio> | ||
| <exit_code range="1:" level="fatal" /> | ||
| </stdio> | ||
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| <command> |
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| <stdio> | |
| <exit_code range="1:" level="fatal" /> | |
| </stdio> | |
| <command> | |
| <command detect_errors="exit_code"> | |
| <inputs> | ||
| <conditional name="inputs"> | ||
| <param name="input" type="select" label="Choose your inputs method" > | ||
| <option value="zip_file" selected="true">Zip file from your history containing your Bruker directories</option> |
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We do have now a bruker filetype that can be used. https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/datatypes_conf.xml.sample#L295
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| </conditional> | ||
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| <param name="bucket_width" label="Bucket width" type="float" value="0.04" help="Default value is 0.04 ppm"/> |
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Would it make sense to add a min/max attribute here and below?
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| <outputs> | ||
| <data format="txt" name="logOut" label="${tool.name}_log" /> | ||
| <data format="tabular" name="sampleOut" label="${tool.name}_sampleMetadata" /> |
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You could add the column names as metadata, for example see here: https://github.com/galaxyproject/tools-iuc/blob/689a4aeaf70a8e77be8589b1dcceb190f9df626a/tools/nonpareil/nonpareil.xml#L84
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| <tests> | ||
| <test> | ||
| <param name="inputs|input" value="zip_file" /> |
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please use the more explicit way of defining nested structures. E.g.
| <param name="inputs|input" value="zip_file" /> | |
| <conditional name="inputs"> | |
| <param name="input" value="zip_file" /> | |
| </conditional> |
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| .. class:: infomark | ||
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| **Authors** Marie Tremblay-Franco ([email protected]), Marion Landi ([email protected]) and Franck Giacomoni ([email protected]) |
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Please use the more explicit schema.org annotations for this: https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-creator-person
The advantage is that Galaxy can nicely render this content and you can access it via the API and such ....
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| --------------------------------------------------- | ||
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| Changelog/News |
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I would remove the changelog its already in the Readme file and its hard to keep it in sync.
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| <?xml version="1.0"?> | |||
| long_description: 'Part of the W4M project: http://workflow4metabolomics.org' | ||
| name: nmr_bucketing | ||
| owner: marie-tremblay-metatoul | ||
| remote_repository_url: https://github.com/workflow4metabolomics/nmr_bucketing |
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Shouldn't this be updated to now point to this repository?
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| categories: [Metabolomics] | |||
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| categories: [Metabolomics] | |
| categories: Metabolomics |
| ################################################################################################ | ||
| # SPECTRA BUCKETING AND INTEGRATION FROM RAW BRUKER FILES # | ||
| # User : Galaxy # | ||
| # Original data : -- # | ||
| # Starting date : 20-10-2014 # | ||
| # Version 1 : 18-12-2014 # | ||
| # Version 2 : 07-01-2015 # | ||
| # Version 3 : 24-10-2016 # | ||
| # # | ||
| # Input files : modification on october 2016 # | ||
| # - Raw bruker files included in user-defined fileName # | ||
| # - Preprocessed files (alignment, ...) included in p x n dataframe # | ||
| ################################################################################################ |
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| ################################################################################################ | |
| # SPECTRA BUCKETING AND INTEGRATION FROM RAW BRUKER FILES # | |
| # User : Galaxy # | |
| # Original data : -- # | |
| # Starting date : 20-10-2014 # | |
| # Version 1 : 18-12-2014 # | |
| # Version 2 : 07-01-2015 # | |
| # Version 3 : 24-10-2016 # | |
| # # | |
| # Input files : modification on october 2016 # | |
| # - Raw bruker files included in user-defined fileName # | |
| # - Preprocessed files (alignment, ...) included in p x n dataframe # | |
| ################################################################################################ |
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Please run some auto formatting tool on this file.
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This could overall be cleaned up into some minimal CRAN package as it has minimal dependencies etc. which would also mkae the Galaxy tool a bit nicer and include all the R functions. That would also make this functionality available to more users or other workflow engines.
| if (fileType=="tsv") | ||
| { | ||
| FileNames <- colnames(fileName) | ||
| n <- length(FileNames) | ||
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| for (i in 1:ncol(fileName)) | ||
| { | ||
| orderedSpectrum <- cbind(as.numeric(rownames(fileName)),fileName[,i]) | ||
| orderedSpectrum <- orderedSpectrum[order(orderedSpectrum[,1],decreasing=T), ] | ||
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| truncatedSpectrum <- orderedSpectrum[orderedSpectrum[,1] < leftBorder & orderedSpectrum[,1] > rightBorder, ] | ||
| truncatedSpectrum[,1] <- round(truncatedSpectrum[,1],3) | ||
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| # Bucketing | ||
| spectrum.bucket <- NmrBrucker_bucket(truncatedSpectrum) | ||
| ppm <- spectrum.bucket[,1] | ||
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| # spectrum Concatenation | ||
| if (i == 1) | ||
| bucketedSpectra <- spectrum.bucket | ||
| if (i > 1) | ||
| bucketedSpectra <- cbind(bucketedSpectra,spectrum.bucket[,2]) | ||
| colnames(bucketedSpectra)[i+1] <- colnames(fileName)[i] | ||
| } | ||
| } |
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Same for this - would be cool if this was its own function.
| runExampleL <- FALSE | ||
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| if(runExampleL) { | ||
| ##------------------------------ | ||
| ## Example of arguments | ||
| ##------------------------------ | ||
| argLs <- list(StudyDir = "Tlse_BPASourisCerveau", | ||
| upper = "10.0", | ||
| lower = "0.50", | ||
| bucket.width = "0.01", | ||
| exclusion = "TRUE", | ||
| exclusion.zone = list(c(6.5,4.5)), | ||
| graph="Overlay") | ||
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| argLs <- c(argLs, | ||
| list(dataMatrixOut = paste(directory,"_NmrBucketing_dataMatrix.tsv",sep=""), | ||
| sampleMetadataOut = paste(directory,"_NmrBucketing_sampleMetadata.tsv",sep=""), | ||
| variableMetadataOut = paste(directory,"_NmrBucketing_variableMetadata.tsv",sep=""), | ||
| graphOut = paste(directory,"_NmrBucketing_graph.pdf",sep=""), | ||
| logOut = paste(directory,"_NmrBucketing_log.txt",sep=""))) | ||
| } |
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| runExampleL <- FALSE | |
| if(runExampleL) { | |
| ##------------------------------ | |
| ## Example of arguments | |
| ##------------------------------ | |
| argLs <- list(StudyDir = "Tlse_BPASourisCerveau", | |
| upper = "10.0", | |
| lower = "0.50", | |
| bucket.width = "0.01", | |
| exclusion = "TRUE", | |
| exclusion.zone = list(c(6.5,4.5)), | |
| graph="Overlay") | |
| argLs <- c(argLs, | |
| list(dataMatrixOut = paste(directory,"_NmrBucketing_dataMatrix.tsv",sep=""), | |
| sampleMetadataOut = paste(directory,"_NmrBucketing_sampleMetadata.tsv",sep=""), | |
| variableMetadataOut = paste(directory,"_NmrBucketing_variableMetadata.tsv",sep=""), | |
| graphOut = paste(directory,"_NmrBucketing_graph.pdf",sep=""), | |
| logOut = paste(directory,"_NmrBucketing_log.txt",sep=""))) | |
| } |
This should be covered in a test case ideally.
| # For parseCommandArgs function | ||
| library(batch) | ||
| # For cumtrapz function | ||
| library(pracma) | ||
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| # R script call | ||
| source_local <- function(fname) | ||
| { | ||
| argv <- commandArgs(trailingOnly = FALSE) | ||
| base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) | ||
| source(paste(base_dir, fname, sep="/")) | ||
| } | ||
| #Import the different functions | ||
| source_local("NmrBucketing_script.R") | ||
| source_local("DrawSpec.R") |
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I think it would be easier to define one function in a file which takes all arguments, then call source on that file in the galaxy wrapper and then call that function. This would remove the entire dependency and command line passing logic. Another options would be to use configfiles.
| ##------------------------------ | ||
| ## Errors ????????????????????? | ||
| ##------------------------------ | ||
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| ##------------------------------ | ||
| ## Constants | ||
| ##------------------------------ | ||
| topEnvC <- environment() | ||
| flagC <- "\n" | ||
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| ##------------------------------ | ||
| ## Script | ||
| ##------------------------------ | ||
| if(!runExampleL) | ||
| argLs <- parseCommandArgs(evaluate=FALSE) | ||
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| ## Parameters Loading | ||
| ##------------------- | ||
| # Inputs | ||
| if (!is.null(argLs[["zipfile"]])){ | ||
| fileType="zip" | ||
| zipfile= argLs[["zipfile"]] | ||
| directory=unzip(zipfile, list=F) | ||
| directory=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/") | ||
| } else if (!is.null(argLs[["tsvfile"]])){ | ||
| fileType="tsv" | ||
| directory <- read.table(argLs[["tsvfile"]],check.names=FALSE,header=TRUE,sep="\t") | ||
| } | ||
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| leftBorder <- argLs[["left_border"]] | ||
| rightBorder <- argLs[["right_border"]] | ||
| bucketSize <- argLs[["bucket_width"]] | ||
| exclusionZones <- argLs[["zone_exclusion_choices.choice"]] | ||
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| exclusionZonesBorders <- NULL | ||
| if (!is.null(argLs$zone_exclusion_left)) | ||
| { | ||
| for(i in which(names(argLs)=="zone_exclusion_left")) | ||
| { | ||
| exclusionZonesBorders <- c(exclusionZonesBorders,list(c(argLs[[i]],argLs[[i+1]]))) | ||
| } | ||
| } | ||
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| graphique <- argLs[["graphType"]] | ||
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| # Outputs | ||
| nomGraphe <- argLs[["graphOut"]] | ||
| dataMatrixOut <- argLs[["dataMatrixOut"]] | ||
| logFile <- argLs[["logOut"]] | ||
| if (fileType=="zip") | ||
| { | ||
| sampleMetadataOut <- argLs[["sampleOut"]] | ||
| variableMetadataOut <- argLs[["variableOut"]] | ||
| } | ||
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| ## Checking R packages | ||
| ##-------------------- | ||
| sink(logFile) | ||
| cat("\t PACKAGE INFO \n") | ||
| pkgs=c("batch","pracma") | ||
| for(pkg in pkgs) { | ||
| suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) | ||
| cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="") | ||
| } | ||
| cat("\n") | ||
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| ## Checking arguments | ||
| ##------------------- | ||
| error.stock <- "\n" | ||
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| if(length(error.stock) > 1) | ||
| stop(error.stock) | ||
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this whole section could be removed without the command line parsing section and if following the approach recommended above.
| data_sample <- outputs[[2]] | ||
| data_variable <- outputs[[3]] | ||
| ppm <- outputs[[4]] | ||
| ppm <- round(ppm,2) |
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Maybe this should be a tool parameter?
Merge the repo https://github.com/workflow4metabolomics/nmr_bucketing to tools-metabolomics
Replace: #187
FOR CONTRIBUTOR: